alg/test/test_sequence.cpp

   1 #include <boost/test/auto_unit_test.hpp>
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4 namespace fs=boost::filesystem;
   5
   6 #include <boost/algorithm/string/case_conv.hpp>
   7
   8 #include <list>
   9 #include <iostream>
  10 #include <sstream>
  11
  12 #include <boost/archive/text_oarchive.hpp>
  13 #include <boost/archive/text_iarchive.hpp>
  14 #include <boost/archive/xml_oarchive.hpp>
  15 #include <boost/archive/xml_iarchive.hpp>
  16
  17 #include "alg/sequence.hpp"
  18 #include "mussa_exceptions.hpp"
  19
  20 using namespace std;
  21
  22 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  23 {
  24         Sequence s;
  25         // make sure that retrieving the sequence doesn't throw an error
  26         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  27 }
  28
  29 //! when we try to load a missing file, do we get an error?
  30 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  31 {
  32   Sequence s;
  33   // there should be errors when we try to load something that doesn't exist
  34   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  35   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  36 }
  37
  38 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  39 {
  40   string header(">Header");
  41   string line1("AAAAGGGGCCCCTTTTT");
  42   string line2("AAAAGGGGCCCCTTTTT");
  43   int seq_len = line1.size() + line2.size();
  44
  45   stringstream cr;
  46   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  47   Sequence seq_cr;
  48   seq_cr.load_fasta(cr);
  49
  50   stringstream crlf;
  51   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
  52   Sequence seq_crlf;
  53   seq_crlf.load_fasta(crlf);
  54
  55   stringstream lf;
  56   lf << header << "\012" << line1 << "\012" << line2 << "\012";
  57   Sequence seq_lf;
  58   seq_lf.load_fasta(lf);
  59
  60   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  61   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
  62   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  63 }
  64
  65
  66 //! Do simple operations work correctly?
  67 BOOST_AUTO_TEST_CASE( sequence_filter )
  68 {
  69   const char *core_seq = "AATTGGCC";
  70   Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
  71   BOOST_CHECK_EQUAL(s1, core_seq);
  72
  73   Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
  74   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
  75   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
  76   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
  77   BOOST_CHECK_EQUAL(s2.size(), s2.size());
  78   //We're currently forcing sequences to uppercase
  79   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
  80
  81   Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
  82   BOOST_CHECK_EQUAL(s3, "ANNNG");
  83   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
  84
  85   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
  86   BOOST_CHECK_EQUAL(s3, "AA");
  87   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
  88   BOOST_CHECK_EQUAL( s3, "GG");
  89   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
  90   BOOST_CHECK_EQUAL( s3, "CCTT");
  91
  92   s3 = "AAGGFF";
  93   BOOST_CHECK_EQUAL(s3, "AAGGNN");
  94 }
  95
  96 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
  97 {
  98   std::string agct("AGCT");
  99   Sequence seq(agct, Sequence::nucleic_alphabet);
 100   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 101   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 102
 103   std::string bdv("BDv");
 104   Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
 105   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 106   // forcing sequence to upper case
 107   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 108                     boost::algorithm::to_upper_copy(bdv));
 109
 110 }
 111
 112 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 113 {
 114   std::string agct("AGCT");
 115   Sequence seq(agct);
 116   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 117   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 118   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 119   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 120   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 121   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 122
 123   std::string bdv("BDv");
 124   Sequence seq_bdv(bdv);
 125   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 126   // default alphabet only allows AGCTUN
 127   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 128 }
 129
 130 BOOST_AUTO_TEST_CASE( subseq_names )
 131 {
 132   Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
 133   s1.set_species("species");
 134   s1.set_fasta_header("a fasta header");
 135   Sequence s2 = s1.subseq(2,2);
 136   BOOST_CHECK_EQUAL(s2, "GG");
 137   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 138   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 139 }
 140
 141 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 142 {
 143   Sequence s1;
 144   BOOST_CHECK_EQUAL( s1.start(), 0 );
 145   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 146
 147   std::string seq_string("AAGGCCTT");
 148   Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
 149   BOOST_CHECK_EQUAL( s2.start(), 0 );
 150   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 151
 152   std::string s3seq_string = seq_string.substr(2,3);
 153   Sequence s3 = s2.subseq(2,3);
 154   BOOST_CHECK_EQUAL( s3.start(), 2);
 155   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 156   BOOST_CHECK_EQUAL( s3.size(), 3);
 157   BOOST_CHECK_EQUAL( s3, s3seq_string);
 158
 159   std::string s4seq_string = s3seq_string.substr(1,1);
 160   Sequence s4 = s3.subseq(1,1);
 161   BOOST_CHECK_EQUAL( s4.start(), 1 );
 162   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 163   BOOST_CHECK_EQUAL( s4.size(), 1);
 164   BOOST_CHECK_EQUAL( s4, s4seq_string);
 165 }
 166
 167 //! Can we load data from a file
 168 BOOST_AUTO_TEST_CASE( sequence_load )
 169 {
 170   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 171   seq_path /=  "human_mck_pro.fa";
 172   Sequence s;
 173   s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
 174   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 175   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 176   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 177                                     "muscle creatine kinase gene (CKMM), "
 178                                     "5' flank");
 179 }
 180
 181 BOOST_AUTO_TEST_CASE( sequence_load_error )
 182 {
 183   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 184   seq_path /= "broken.fa";
 185   bool exception_thrown = false;
 186   std::string exception_filename;
 187   Sequence s;
 188   try {
 189     s.load_fasta(seq_path);
 190   } catch(sequence_invalid_load_error e) {
 191     exception_thrown = true;
 192     size_t native_string_size = seq_path.native_file_string().size();
 193     std:string estr(e.what());
 194     BOOST_REQUIRE(estr.size() > native_string_size);
 195     std::copy(estr.begin(), estr.begin()+native_string_size,
 196               std::back_inserter(exception_filename));
 197   }
 198   BOOST_CHECK_EQUAL(exception_thrown, true);
 199   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 200 }
 201
 202 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 203 {
 204   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 205   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 206   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 207   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 208   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 209   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 210   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 211   std::stringstream garbage_fasta(garbage_string);
 212
 213   Sequence s;
 214   s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
 215   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 216                                  Sequence::reduced_dna_alphabet),
 217                     sequence_invalid_load_error);
 218   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 219                                  Sequence::reduced_dna_alphabet),
 220                     sequence_invalid_load_error);
 221   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 222                                  Sequence::reduced_dna_alphabet),
 223                     sequence_invalid_load_error);
 224
 225 }
 226
 227 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 228 {
 229   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 230   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 231   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 232   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 233   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 234   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 235   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 236   std::stringstream garbage_fasta(garbage_string);
 237
 238   Sequence s;
 239   s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
 240   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 241                                  Sequence::reduced_rna_alphabet),
 242                     sequence_invalid_load_error);
 243   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 244                                  Sequence::reduced_rna_alphabet),
 245                     sequence_invalid_load_error);
 246   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 247                                  Sequence::reduced_rna_alphabet),
 248                     sequence_invalid_load_error);
 249 }
 250
 251 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 252 {
 253   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 254   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 255   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 256   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 257   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 258   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 259   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 260   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 261   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 262   std::stringstream garbage_fasta(garbage_string);
 263
 264   Sequence s;
 265   Sequence specific;
 266   // there's two copies of reduced_rna_fasta because i didn't feel like
 267   // figuring out how to properly reset the read pointer in a stringstream
 268   s.load_fasta(reduced_rna_fasta1);
 269   specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
 270   BOOST_CHECK_EQUAL(s, specific);
 271
 272   s.load_fasta(reduced_dna_fasta1);
 273   specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
 274   BOOST_CHECK_EQUAL(s, specific);
 275
 276   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 277                     sequence_invalid_load_error);
 278   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 279                     sequence_invalid_load_error);
 280 }
 281
 282 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 283 {
 284   std::string fasta_file(
 285     ">gi|10129974|gb|AF188002.1|AF188002\n"
 286     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 287     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 288     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 289     ">gi|1621|emb|X55146.1|OCMCK1\n"
 290     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 291   );
 292   istringstream seq1_file(fasta_file);
 293   Sequence seq1;
 294   seq1.load_fasta(seq1_file, 1, 0, 0);
 295   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 296
 297   istringstream seq2_file(fasta_file);
 298   Sequence seq2;
 299   seq2.load_fasta(seq2_file, 2, 0, 0);
 300   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 301
 302   istringstream seq3_file(fasta_file);
 303   Sequence seq3;
 304   seq3.load_fasta(seq3_file, 3, 0, 0);
 305   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 306 }
 307
 308 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 309 {
 310   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 311   Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
 312   Sequence seqr = seq.rev_comp();
 313
 314   BOOST_CHECK( seq != seqr );
 315   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 316   // forcing sequence to upper case
 317   BOOST_CHECK_EQUAL( seq.get_sequence(),
 318                      boost::algorithm::to_upper_copy(iupac_symbols) );
 319 }
 320
 321 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 322 {
 323   std::string dna_str("AGCTN");
 324   Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
 325   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 326   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 327 }
 328
 329 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 330 {
 331   std::string rna_str("AGCUN");
 332   Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
 333   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
 334   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 335 }
 336
 337 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 338 {
 339   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 340   Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
 341   Sequence subseq = seq.subseq(8,4);
 342   BOOST_CHECK_EQUAL( subseq, "AAGG");
 343   Sequence rev_subseq = subseq.rev_comp();
 344   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 345   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 346 }
 347
 348 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 349 {
 350   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 351   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 352   Sequence seq(dna_str);
 353   std::string seq_reversed(seq.rbegin(), seq.rend());
 354   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 355
 356   std::string substr = dna_str.substr(8,4);
 357   Sequence subseq = seq.subseq(8,4);
 358   BOOST_CHECK_EQUAL(substr, subseq);
 359
 360   std::string substr_reversed(substr.rbegin(), substr.rend());
 361   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 362   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 363 }
 364
 365 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 366 {
 367   // so what happens with reverse interators when we have no sequence?
 368   Sequence seq1;
 369   Sequence seq2;
 370   Sequence seq3("AGCT");
 371
 372   // all the empty sequences should have equal iterators
 373   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 374   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 375
 376   // none of the seq1 iterators should equal any of the seq3 iterators
 377   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 378   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 379   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 380   BOOST_CHECK(seq1.rend() != seq3.rend());
 381
 382   // seq3 iterators should work
 383   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 384
 385 }
 386
 387 BOOST_AUTO_TEST_CASE( annotation_load )
 388 {
 389   string annot_data = "human\n"
 390                       "0 10 name   type\n"
 391                       "10 20 myf7\n"
 392                       "20 30 myod\n"
 393                       "50\t55 anothername\n"
 394                       "60 50 backward\n"
 395                       ">ident3 asdf\n"
 396                       "GCT\n"
 397                       "gCTn\n"
 398                       "75\t90\tname2\ttype2\n"
 399                       "100 120 name-asdf type!@#$%\n"
 400                       ;
 401   string s(100, 'A');
 402   s += "GCTGCTAATT";
 403   Sequence seq(s, Sequence::reduced_dna_alphabet);
 404
 405   //istringstream annot_stream(annot_data);
 406   seq.parse_annot(annot_data, 0, 0);
 407   std::list<annot> annots_list = seq.annotations();
 408   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 409   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 410   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 411   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 412   BOOST_CHECK_EQUAL( annots[0].type, "type");
 413   BOOST_CHECK_EQUAL( annots[0].name, "name");
 414   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 415   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 416   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 417   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 418   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 419   BOOST_CHECK_EQUAL( annots[5].end, 90);
 420   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 421   BOOST_CHECK_EQUAL( annots[6].end, 120);
 422   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 423   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 424   // sequence defined annotations will always be after the
 425   // absolute positions
 426   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 427   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 428
 429   //BOOST_CHECK_EQUAL( annots
 430 }
 431
 432 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 433 {
 434   string annot_data = "human\n"
 435                       "0 10 name   type\n"
 436                       "blah60 50 backward\n"
 437                       ">ident3 asdf\n"
 438                       "GCT\n"
 439                       "gCTn\n"
 440                       ;
 441   string s(100, 'A');
 442   s += "GCTGCTAATT";
 443   Sequence seq(s, Sequence::reduced_dna_alphabet);
 444
 445   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 446   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 447   }
 448
 449 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 450 {
 451   // this actually is basically what's returned by UCSC
 452   // (well actually with some of the sequence and copies of fasta blocks
 453   // removed to make the example shorter
 454   string annot_data = "\n"
 455     "<PRE>\n"
 456     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 457     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 458     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 459     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 460     "</PRE>\n"
 461     "\n"
 462     "</BODY>\n"
 463     "</HTML>\n"
 464     ;
 465
 466   string s =
 467     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 468     "AAAAA"
 469     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 470   Sequence seq(s, Sequence::reduced_dna_alphabet);
 471   seq.parse_annot(annot_data);
 472   std::list<annot> annots = seq.annotations();
 473   BOOST_CHECK_EQUAL( annots.size(), 2);
 474 }
 475
 476 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 477 {
 478   string annot_data = "0 10 name   type\n"
 479                       "10 20 myf7\n"
 480                       "20 30 myod\n"
 481                       "50\t55 anothername\n"
 482                       "60 50 backward\n"
 483                       ">ident3 asdf\n"
 484                       "GCT\n"
 485                       "gCTn\n"
 486                       "75\t90\tname2\ttype2\n"
 487                       "100 120 name-asdf type!@#$%\n"
 488                       ;
 489   string s(100, 'A');
 490   s += "GCTGCTAATT";
 491   Sequence seq(s, Sequence::reduced_dna_alphabet);
 492
 493   //istringstream annot_stream(annot_data);
 494   seq.parse_annot(annot_data, 0, 0);
 495   std::list<annot> annots_list = seq.annotations();
 496   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 497   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 498   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 499   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 500   BOOST_CHECK_EQUAL( annots[0].type, "type");
 501 }
 502
 503 // ticket:83 when you try to load a sequence from a file that doesn't
 504 // have fasta headers it crashes.
 505 BOOST_AUTO_TEST_CASE( sequence_past_end )
 506 {
 507   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 508   seq_path /=  "misformated_seq.fa";
 509   Sequence s;
 510   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 511 }
 512
 513 BOOST_AUTO_TEST_CASE ( sequence_empty )
 514 {
 515
 516   Sequence s;
 517   BOOST_CHECK_EQUAL( s.empty(), true );
 518   s = "AAAGGG";
 519   BOOST_CHECK_EQUAL( s.empty(), false );
 520   s.clear();
 521   BOOST_CHECK_EQUAL( s.empty(), true);
 522   s = "";
 523   BOOST_CHECK_EQUAL( s.empty(), true);
 524 }
 525
 526 BOOST_AUTO_TEST_CASE ( sequence_size )
 527 {
 528
 529   Sequence s;
 530   BOOST_CHECK_EQUAL( s.size(), 0);
 531   std::string seq_string("AAAGGG");
 532   s = seq_string;
 533   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 534   s.clear();
 535   BOOST_CHECK_EQUAL( s.size(), 0);
 536   s = "";
 537   BOOST_CHECK_EQUAL( s.size(), 0);
 538 }
 539
 540 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 541 {
 542   Sequence szero("", Sequence::reduced_dna_alphabet);
 543   BOOST_CHECK_EQUAL(szero.empty(), true);
 544   BOOST_CHECK_EQUAL(szero, szero);
 545   BOOST_CHECK_EQUAL(szero, "");
 546
 547   Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
 548   sclear.clear();
 549   BOOST_CHECK_EQUAL(sclear.empty(), true);
 550   BOOST_CHECK_EQUAL(sclear, sclear);
 551   BOOST_CHECK_EQUAL(sclear, szero);
 552   BOOST_CHECK_EQUAL(sclear, "");
 553
 554 }
 555 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 556 {
 557   std::string seq_string = "AAGGCCTTNNTATA";
 558   Sequence s(seq_string, Sequence::reduced_dna_alphabet);
 559   const Sequence cs(s);
 560   std::string::size_type count = 0;
 561
 562   std::string::iterator str_itor;
 563   Sequence::const_iterator s_itor;
 564   Sequence::const_iterator cs_itor;
 565
 566   for( str_itor = seq_string.begin(),
 567        s_itor   = s.begin(),
 568        cs_itor  = cs.begin();
 569        str_itor != seq_string.end() and
 570        s_itor   != s.end() and
 571        cs_itor  != cs.end();
 572        ++str_itor, ++s_itor, ++cs_itor, ++count)
 573   {
 574     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 575     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 576     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 577   }
 578   BOOST_CHECK_EQUAL( seq_string.size(), count );
 579   BOOST_CHECK_EQUAL( s.size(), count );
 580   BOOST_CHECK_EQUAL( cs.size(), count );
 581 }
 582
 583 BOOST_AUTO_TEST_CASE( sequence_motifs )
 584 {
 585   string m("AAAA");
 586   string bogus("AATTGGAA");
 587   Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
 588
 589   list<motif>::const_iterator motif_i = s1.motifs().begin();
 590   list<motif>::const_iterator motif_end = s1.motifs().end();
 591
 592   // do our iterators work?
 593   BOOST_CHECK( motif_i == s1.motifs().begin() );
 594   BOOST_CHECK( motif_end == s1.motifs().end() );
 595   BOOST_CHECK( motif_i == motif_end );
 596
 597   // this shouldn't show up
 598   s1.add_motif(bogus);
 599   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 600   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 601
 602   s1.add_motif(m);
 603   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 604   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 605
 606   for(motif_i = s1.motifs().begin();
 607       motif_i != s1.motifs().end();
 608       ++motif_i)
 609   {
 610     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 611     BOOST_CHECK_EQUAL( motif_i->name, m);
 612     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 613   }
 614
 615   s1.clear_motifs();
 616   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 617
 618   /* FIXME: enable this when i find a way of passing storing the motif name
 619   // does our annotation travel?
 620   Sequence motif_seq(m);
 621   motif_seq.set_fasta_header("hi");
 622   s1.add_motif(motif_seq);
 623
 624   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 625   for(motif_i = s1.motifs().begin();
 626       motif_i != s1.motifs().end();
 627       ++motif_i)
 628   {
 629     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 630     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 631     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 632   }
 633   */
 634 }
 635
 636 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 637 {
 638   // when searching for a motif on a subsequence we should
 639   // only search the subsequence ticket:199
 640   string aaaa("AAAA");
 641   string cccc("CCCC");
 642   Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
 643
 644   // this shouldn't show up
 645   s1.add_motif(cccc);
 646   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 647
 648   s1.add_motif(aaaa);
 649   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 650
 651   Sequence subseq1 = s1.subseq(4,5);
 652   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 653   subseq1.clear_motifs();
 654   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 655   // this is outside of our subsequence, and so shouldn't be found
 656   subseq1.add_motif(aaaa);
 657   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 658
 659   subseq1.add_motif(cccc);
 660   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 661   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 662   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 663   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 664   BOOST_CHECK_EQUAL(motif_i->end, 5);
 665 }
 666
 667 BOOST_AUTO_TEST_CASE( annot_test )
 668 {
 669   annot a(0, 10, "test", "thing");
 670
 671   BOOST_CHECK_EQUAL( a.begin, 0 );
 672   BOOST_CHECK_EQUAL( a.end,   10 );
 673   BOOST_CHECK_EQUAL( a.type,  "test" );
 674   BOOST_CHECK_EQUAL( a.name,  "thing" );
 675
 676   motif m(10, "AAGGCC");
 677   BOOST_CHECK_EQUAL( m.begin, 10 );
 678   BOOST_CHECK_EQUAL( m.type, "motif" );
 679   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 680   BOOST_CHECK_EQUAL( m.end,  10+6 );
 681 }
 682
 683 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 684 {
 685   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 686            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 687            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 688            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 689            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 690            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 691            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 692            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 693   string gc("GCCCCC");
 694   string gga("GGACACCTC");
 695   Sequence seq(s, Sequence::reduced_dna_alphabet);
 696
 697   std::list<Sequence> query_list;
 698   std::list<string> string_list;
 699   query_list.push_back(Sequence(gc));
 700   string_list.push_back(gc);
 701   query_list.push_back(Sequence(gga));
 702   string_list.push_back(gga);
 703
 704   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 705   seq.find_sequences(query_list.begin(), query_list.end());
 706
 707   int count = 0;
 708   for(list<string>::iterator string_i = string_list.begin();
 709       string_i != string_list.end();
 710       ++string_i)
 711   {
 712     string::size_type pos=0;
 713     while(pos != string::npos) {
 714       pos = s.find(*string_i, pos);
 715       if (pos != string::npos) {
 716         ++count;
 717         ++pos;
 718       }
 719     }
 720   }
 721   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 722   const std::list<annot> &a = seq.annotations();
 723   for (std::list<annot>::const_iterator annot_i = a.begin();
 724        annot_i != a.end();
 725        ++annot_i)
 726   {
 727     int count = annot_i->end - annot_i->begin ;
 728   }
 729 }
 730
 731 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 732 {
 733   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 734            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 735            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 736            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 737            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 738            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 739            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 740            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 741   Sequence seq(s, Sequence::reduced_dna_alphabet);
 742
 743
 744   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 745   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 746   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 747   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 748   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 749
 750   Sequence subseq = seq.subseq(5, 10);
 751   const list<annot> annots = subseq.annotations();
 752   // generate some ground truth
 753   list<annot> correct;
 754   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 755   correct.push_back(annot(5,10, "10-20", "10-20"));
 756   correct.push_back(annot(0,10, "0-20",  "0-20"));
 757   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 758   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 759
 760   list<annot>::iterator correct_i = correct.begin();
 761   list<annot>::const_iterator annot_i = annots.begin();
 762   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 763   {
 764     BOOST_CHECK( *annot_i == *correct_i );
 765   }
 766 }
 767
 768 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 769 {
 770   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 771            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 772            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 773            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 774            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 775            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 776            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 777            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 778   Sequence seq(s, Sequence::reduced_dna_alphabet);
 779
 780   // starting conditions
 781   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 782   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 783   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 784   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 785   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 786   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 787   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 788   seq.add_motif("CCGTCCC");
 789   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 790   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 791   seq.clear_motifs();
 792   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 793   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 794 }
 795
 796 BOOST_AUTO_TEST_CASE( out_operator )
 797 {
 798   string s("AAGGCCTT");
 799   Sequence seq(s, Sequence::reduced_dna_alphabet);
 800
 801   ostringstream buf;
 802   buf << s;
 803   BOOST_CHECK_EQUAL( s, buf.str() );
 804 }
 805
 806 BOOST_AUTO_TEST_CASE( get_name )
 807 {
 808   Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
 809
 810   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 811   seq.set_species("hooman"); // anyone remember tradewars?
 812   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 813   seq.set_fasta_header("fasta human");
 814   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 815 }
 816
 817 BOOST_AUTO_TEST_CASE( serialize_simple )
 818 {
 819   std::string seq_string = "AAGGCCTT";
 820   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 821   seq.set_species("ribbet");
 822   std::ostringstream oss;
 823   // allocate/deallocate serialization components
 824   {
 825     boost::archive::text_oarchive oarchive(oss);
 826     const Sequence& const_seq(seq);
 827     BOOST_CHECK_EQUAL(seq, const_seq);
 828     oarchive << const_seq;
 829   }
 830   Sequence seq_loaded;
 831   {
 832     std::istringstream iss(oss.str());
 833     boost::archive::text_iarchive iarchive(iss);
 834     iarchive >> seq_loaded;
 835   }
 836   BOOST_CHECK_EQUAL(seq_loaded, seq);
 837   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 838 }
 839
 840 BOOST_AUTO_TEST_CASE( serialize_tree )
 841 {
 842   std::string seq_string = "AAGGCCTT";
 843   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 844   seq.set_species("ribbet");
 845   seq.add_motif("AA");
 846   seq.add_motif("GC");
 847   annot a1(6,7,"t","t");
 848   seq.add_annotation(a1);
 849
 850   std::ostringstream oss;
 851   // allocate/deallocate serialization components
 852   {
 853     boost::archive::text_oarchive oarchive(oss);
 854     const Sequence& const_seq(seq);
 855     BOOST_CHECK_EQUAL(seq, const_seq);
 856     oarchive << const_seq;
 857   }
 858
 859   Sequence seq_loaded;
 860   {
 861     std::istringstream iss(oss.str());
 862     boost::archive::text_iarchive iarchive(iss);
 863     iarchive >> seq_loaded;
 864   }
 865   BOOST_CHECK_EQUAL(seq_loaded, seq);
 866 }
 867
 868 // this writes out an "old" style annotated sequence
 869 // with annotations attached as "motifs" and "annots"
 870 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 871 {
 872   std::string seq_string = "AAGGCCTT";
 873   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 874   seq.set_species("ribbet");
 875   seq.add_motif("AA");
 876   seq.add_motif("GC");
 877   annot a1(6,7,"t","t");
 878   seq.add_annotation(a1);
 879
 880   std::ostringstream oss;
 881   // allocate/deallocate serialization components
 882   {
 883     boost::archive::xml_oarchive oarchive(oss);
 884     const Sequence& const_seq(seq);
 885     BOOST_CHECK_EQUAL(seq, const_seq);
 886     oarchive << boost::serialization::make_nvp("root", const_seq);
 887   }
 888   Sequence seq_loaded;
 889   {
 890     std::istringstream iss(oss.str());
 891     boost::archive::xml_iarchive iarchive(iss);
 892     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 893   }
 894   BOOST_CHECK_EQUAL(seq_loaded, seq);
 895 }
 896
 897 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 898 {
 899   std::string seq_string = "AAGGCCTT";
 900   Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
 901   Sequence seq2(seq1);
 902
 903   std::ostringstream oss;
 904   // allocate/deallocate serialization components
 905   {
 906     boost::archive::xml_oarchive oarchive(oss);
 907     const Sequence& const_seq1(seq1);
 908     const Sequence& const_seq2(seq2);
 909     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 910     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 911   }
 912   //std::cout << "xml: " << oss.str() << std::endl;
 913   Sequence seq1_loaded;
 914   Sequence seq2_loaded;
 915   {
 916     std::istringstream iss(oss.str());
 917     boost::archive::xml_iarchive iarchive(iss);
 918     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 919     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 920   }
 921   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 922   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 923   // test if our pointers are the same
 924   BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());
 925 }